Reference SNP(refSNP) Cluster Report: rs685404

Reference SNP(refSNP) Cluster Report: rs685404

refSNP ID: rs685404
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	G/T
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_000231.1:c.0-6020T>G
NT_024524.13:g.4751814T>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1479967 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs685404 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Success Rate
ss859061	SC_JCM\|AL356287.3_19868	rev/T	A/C	ttttttaaacttagctttatatttccacag	tttatcactctgtggtgttttctaagatct	07/27/00	10/10/03	83	Genomic	unknown
ss980735	KWOK\|OVLP-000804-579295	rev/T	A/C	ttttttaaacttagctttatatttccacag	tttatcactctgtggtgttttctaagatct	09/01/00	10/10/03	86	Genomic	99 %
ss1479967	TSC-CSHL\|TSC0098757	fwd/B	G/T	agatcttagaaaacaccacagagtgataaa	ctgtggaaatataaagctaagtttaaaaaa	09/07/00	10/25/06	92	Genomic	95 %
ss1600915	KWOK\|OVLP-000925-360362	rev/T	A/C	ttttttaaacttagctttatatttccacag	tttatcactctgtggtgttttctaagatct	10/04/00	10/10/03	87	Genomic	99 %
ss2603452	SC_JCM\|AL160256.6_6735	rev/T	A/C	ttttttaaacttagctttatatttccacag	tttatcactctgtggtgttttctaagatct	11/03/00	10/10/03	92	Genomic	unknown
ss13255293	SC_SNP\|NT_009799.12_4751814	fwd/B	G/T	agatcttagaaaacaccacagagtgataaa	ctgtggaaatataaagctaagtttaaaaaa	10/22/03	02/27/04	119	Genomic	unknown
ss19278064	CSHL-HAPMAP\|CSHL-HuDD-200402.chr13.NT_024524.13_4751814	fwd/B	G/T	agatcttagaaaacaccacagagtgataaa	ctgtggaaatataaagctaagtttaaaaaa	02/20/04	03/04/04	120	Genomic	unknown
ss21115679	SSAHASNP\|WGSA-200403-chr13.chr13.NT_024524.13_4751814	fwd/B	G/T	agatcttagaaaacaccacagagtgataaa	ctgtggaaatataaagctaagtttaaaaaa	03/19/04	03/19/04	121	Genomic	unknown
ss40328204	ABI\|hCV2702385	fwd/B	G/T	agatcttagaaaacaccacagagtgataaa	ctgtggaaatataaagctaagtttaaaaaa	07/16/05	07/16/05	126	Genomic	unknown
ss69127715	PERLEGEN\|PGP06384714	fwd/B	G/T	agatcttagaaaacaccacagagtgataaa	ctgtggaaatataaagctaagtttaaaaaa	01/30/07	08/14/07	127	Genomic	unknown
ss75132364	ILLUMINA\|ILMN_Human_1M_rs685404	fwd/B	G/T	agatcttagaaaacaccacagagtgataaa	ctgtggaaatataaagctaagtttaaaaaa	08/28/07	08/29/07	129	Genomic	unknown
ss78841174	HGSV\|Cor18507_SNV_20070510.chr13_22669814	fwd/B	G/T	agatcttagaaaacaccacagagtgataaa	ctgtggaaatataaagctaagtttaaaaaa	10/19/07	10/21/07	129	Genomic	unknown
ss89526863	BCMHGSC_JDW\|JWB-0639531	fwd/B	G/T	agatcttagaaaacaccacagagtgataaa	ctgtggaaatataaagctaagtttaaaaaa	02/26/08	02/28/08	129	Genomic	unknown

Fasta sequence (Legend)

 CGTGTGACCC AACAAGCACT TACTGATTGC CTATTATGTG CACATAACTG ATACTGGTCA
 CGGTCACCTA GTCACATCGT TGTAATTGAC TTCTCACGTG GGTTACCTTG TCATTTGGAG
 GGACGATGCA CCATGATGGT GCTTGTTACC TAGTAAGAAA TTATCTATCT GGATATTAGA
 GCTAGGTGAC ATGGCTTATG AAAGACAGTT TTTGAAACTG TGGAAAGTAA TTTTTCAGGA
 GTTTTCAGAT TGACATCATA AGTGCTATAA GAGGTTTGCT AAGCCCTCAG TCAGCAAGCC
 CTGTGAACGG AAAGGACCTT ACCCAAGGCA GGTAGAATGC CATCGCTAAC ACTCAGGTGA
 ATCTCCCATG AAGATTAGAA AGATGGCTTA CTCTCTTATC TGACAGATTG CATACAGCTG
 CAAAGAGAAT TAGTATATTG GAAGGTAGAT CTTAGAAAAC ACCACAGAGT GATAAA
 K
 CTGTGGAAAT ATAAAGCTAA GTTTAAAAAA CATGACTGGT GAATGAGGAG GTCTAAATAT
 ATCTTATTGA AGCCCCAGTG GAAGTAACCG GAGAAAATAT AGGAAAGACA ATGGTTAAAT
 AAGCAATTGC CAAGAGTTTT CTATAACTGA AGACAAGTTC AATTGAAAAC AGACACTGAC
 TCATGAACAG AATAAATTAA TTCAAATTTA TGAAATGAAA TCATTCTGAA TCTGGAAAAC
 ACTAAAAGTA AAGAAACTTT TAAAAGTCCC AATGGAAAAA AAAAGACGTA ACACTGAAAA
 AAACTTTGTA GATACATGTT GAATGAACTG TTGAAAGCAA AGTGGTGGAA ATTTGTACCA
 GAAAAACATT GAAACCAAAA GTGGCATACC AAAGTCAGTA TCAGACAGAT AACTTTGAAC
 TATTATAACT CATTCTTTGA GTTCTTAGAT AGAATTAAAT GTCATTTCTA AAAGGTCTGT
 TTTGTTCTTT CTCAAACTCA CCTTTTCAAA AATCATATGA TATTAACACG TTTGGGCATT
 ATTCTTGCAT TTATCATCTT TGTGTCTCAG ACTCTTGATA ATGGCCTACC CAAACTAGGC
 ATGACAATAA ATGTTGGTTG AAATGAAGAA TGTCATGAAG ACACTATGTT CGATTCACTA
 TATTATATGC TATGACAAGA ATCACATAAT GTAGAAGACA GATTATCTGT CCTTAAGGTC
 ATTTTGTTTT AAATAACAAA CTGGGGATCA TGAATTCAGA AGCATATAAA AGCAGATATT
 TACACCAAAA CAAGTATAGT GCTTCACATC TGGAGCCCTA TCCATTAAAG GATTGAAAAC
 TAAGCTGAGA GATGCAAGCT AAAGTAGGTA TAGGCCCAAG GC

GeneView

GeneView via analysis of contig annotation: SGCG sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_024524->NM_000231

function

HuRef

NW_001838070->NM_000231

function

Celera

NW_925473->NM_000231

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_024524->NM_000231->NP_000222	4751814	forward	intron

HuRef	NW_001838070->NM_000231->NP_000222	137352	forward	intron

Celera	NW_925473->NM_000231->NP_000222	4570050	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs685404 maps exactly once on NCBI human chromosome 13

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
13	NW_001838070.1	137352	4585227	plus	G	alt_assembly_8	HuRef	HuRef	view	476
13	NW_925473.1	4570050	4834826	plus	G	alt_assembly_1	Celera	Celera	view	476
13	NT_024524.13	4751814	22669814	plus	T	ref_assembly	reference	reference	view	476

NCBI Resource Links

Submitter-Referenced
GenBank
NT_024524 AL160256 AL356287 AL356287.3 AL356287.4

dbSNP Blast Analysis
GenBank HTGS Finished:
AL356287.16 NC_000013.9

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss1479967	HapMap-CEU	European	112	IG	0.393	0.393	0.214	0.200	0.589	0.411

	HapMap-HCB	Asian	90	IG	0.133	0.467	0.400	1.000	0.367	0.633

	HapMap-JPT	Asian	90	IG	0.133	0.622	0.244		0.444	0.556

	HapMap-YRI	Sub-Saharan African	118	IG	0.254	0.492	0.254	1.000	0.500	0.500

ss69127715	HapMap-CEU	European	120	GF	0.383	0.433	0.183		0.600	0.400

	HapMap-HCB	Asian	90	GF	0.200	0.467	0.333		0.433	0.567

	HapMap-JPT	Asian	90	GF	0.133	0.689	0.178		0.478	0.522

	HapMap-YRI	Sub-Saharan African	120	GF	0.250	0.550	0.200		0.525	0.475

Concordant Genotype	Total Sample	G/G	G/T	T/T
ss1479967	241	55	121	58
ss69127715	241	55	128	58

RefSNP Genotype Summary	Total Individual	G/G	G/T	T/T
rs685404	270	55	128	58

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
150	ss1479967	T/T	CSHL-HAPMAP	HapMap-CEU	NA10846	CEPH1334.01	r23_ch13_CEU_perlegen:genotyping_1.0.0	4880593
150	ss69127715	G/T	CSHL-HAPMAP	HapMap-CEU	NA10846	CEPH1334.01	chr13-HapMap-CEU
161	ss1479967	G/G	CSHL-HAPMAP	HapMap-CEU	NA07029	CEPH1340.01	r23_ch13_CEU_perlegen:genotyping_1.0.0	4880593
161	ss69127715	G/T	CSHL-HAPMAP	HapMap-CEU	NA07029	CEPH1340.01	chr13-HapMap-CEU
171	ss1479967	G/T	CSHL-HAPMAP	HapMap-CEU	NA07022	CEPH1340.11	r23_ch13_CEU_perlegen:genotyping_1.0.0	4880593
171	ss69127715	G/G	CSHL-HAPMAP	HapMap-CEU	NA07022	CEPH1340.11	chr13-HapMap-CEU
252	ss1479967	G/T	CSHL-HAPMAP	HapMap-CEU	NA11839	CEPH1349.13	r23_ch13_CEU_perlegen:genotyping_1.0.0	4880593
252	ss69127715	G/G	CSHL-HAPMAP	HapMap-CEU	NA11839	CEPH1349.13	chr13-HapMap-CEU
362	ss1479967	G/T	CSHL-HAPMAP	HapMap-CEU	NA11994	CEPH1362.15	r23_ch13_CEU_perlegen:genotyping_1.0.0	4880593
362	ss69127715	G/G	CSHL-HAPMAP	HapMap-CEU	NA11994	CEPH1362.15	chr13-HapMap-CEU
410	ss1479967	T/T	CSHL-HAPMAP	HapMap-CEU	NA12155	CEPH1408.12	r23_ch13_CEU_perlegen:genotyping_1.0.0	4880593
410	ss69127715	G/T	CSHL-HAPMAP	HapMap-CEU	NA12155	CEPH1408.12	chr13-HapMap-CEU
411	ss1479967	G/G	CSHL-HAPMAP	HapMap-CEU	NA12156	CEPH1408.13	r23_ch13_CEU_perlegen:genotyping_1.0.0	4880593
411	ss69127715	G/T	CSHL-HAPMAP	HapMap-CEU	NA12156	CEPH1408.13	chr13-HapMap-CEU
548	ss1479967	G/G	CSHL-HAPMAP	HapMap-CEU	NA12763	CEPH1447.12	r23_ch13_CEU_perlegen:genotyping_1.0.0	4880593
548	ss69127715	G/T	CSHL-HAPMAP	HapMap-CEU	NA12763	CEPH1447.12	chr13-HapMap-CEU
565	ss1479967	G/G	CSHL-HAPMAP	HapMap-CEU	NA12801	CEPH1454.01	r23_ch13_CEU_perlegen:genotyping_1.0.0	4880593
565	ss69127715	G/T	CSHL-HAPMAP	HapMap-CEU	NA12801	CEPH1454.01	chr13-HapMap-CEU
5141	ss1479967	T/T	CSHL-HAPMAP	HapMap-YRI	NA19098	YOR105.03	r23_ch13_YRI_perlegen:genotyping_1.0.0	4880593
5141	ss69127715	G/T	CSHL-HAPMAP	HapMap-YRI	NA19098	YOR105.03	chr13-HapMap-YRI
5142	ss1479967	G/T	CSHL-HAPMAP	HapMap-YRI	NA19194	YOR112.01	r23_ch13_YRI_perlegen:genotyping_1.0.0	4880593
5142	ss69127715	G/G	CSHL-HAPMAP	HapMap-YRI	NA19194	YOR112.01	chr13-HapMap-YRI
5146	ss1479967	G/T	CSHL-HAPMAP	HapMap-YRI	NA19238	YOR117.02	r23_ch13_YRI_perlegen:genotyping_1.0.0	4880593
5146	ss69127715	G/G	CSHL-HAPMAP	HapMap-YRI	NA19238	YOR117.02	chr13-HapMap-YRI
5160	ss1479967	T/T	CSHL-HAPMAP	HapMap-HCB	NA18545	CH18545	r23_ch13_HCB_perlegen:genotyping_1.0.0	4880593
5160	ss69127715	G/T	CSHL-HAPMAP	HapMap-HCB	NA18545	CH18545	chr13-HapMap-HCB
5161	ss1479967	G/T	CSHL-HAPMAP	HapMap-HCB	NA18572	CH18572	r23_ch13_HCB_perlegen:genotyping_1.0.0	4880593
5161	ss69127715	G/G	CSHL-HAPMAP	HapMap-HCB	NA18572	CH18572	chr13-HapMap-HCB
5162	ss1479967	T/T	CSHL-HAPMAP	HapMap-HCB	NA18547	CH18547	r23_ch13_HCB_perlegen:genotyping_1.0.0	4880593
5162	ss69127715	G/T	CSHL-HAPMAP	HapMap-HCB	NA18547	CH18547	chr13-HapMap-HCB
5167	ss1479967	T/T	CSHL-HAPMAP	HapMap-HCB	NA18611	CH18611	r23_ch13_HCB_perlegen:genotyping_1.0.0	4880593
5167	ss69127715	G/T	CSHL-HAPMAP	HapMap-HCB	NA18611	CH18611	chr13-HapMap-HCB
5178	ss1479967	G/T	CSHL-HAPMAP	HapMap-HCB	NA18622	CH18622	r23_ch13_HCB_perlegen:genotyping_1.0.0	4880593
5178	ss69127715	G/G	CSHL-HAPMAP	HapMap-HCB	NA18622	CH18622	chr13-HapMap-HCB
5189	ss1479967	G/T	CSHL-HAPMAP	HapMap-HCB	NA18592	CH18592	r23_ch13_HCB_perlegen:genotyping_1.0.0	4880593
5189	ss69127715	G/G	CSHL-HAPMAP	HapMap-HCB	NA18592	CH18592	chr13-HapMap-HCB
5209	ss1479967	T/T	CSHL-HAPMAP	HapMap-JPT	NA18960	JA18960	r23_ch13_JPT_perlegen:genotyping_1.0.0	4880593
5209	ss69127715	G/G	CSHL-HAPMAP	HapMap-JPT	NA18960	JA18960	chr13-HapMap-JPT
5220	ss1479967	G/G	CSHL-HAPMAP	HapMap-JPT	NA18980	JA18980	r23_ch13_JPT_perlegen:genotyping_1.0.0	4880593
5220	ss69127715	G/T	CSHL-HAPMAP	HapMap-JPT	NA18980	JA18980	chr13-HapMap-JPT
5228	ss1479967	T/T	CSHL-HAPMAP	HapMap-JPT	NA18994	JA18994	r23_ch13_JPT_perlegen:genotyping_1.0.0	4880593
5228	ss69127715	G/T	CSHL-HAPMAP	HapMap-JPT	NA18994	JA18994	chr13-HapMap-JPT
5234	ss1479967	T/T	CSHL-HAPMAP	HapMap-JPT	NA18999	JA18999	r23_ch13_JPT_perlegen:genotyping_1.0.0	4880593
5234	ss69127715	G/T	CSHL-HAPMAP	HapMap-JPT	NA18999	JA18999	chr13-HapMap-JPT
5252	ss1479967	G/G	CSHL-HAPMAP	HapMap-YRI	NA18522	YOR016.03	r23_ch13_YRI_perlegen:genotyping_1.0.0	4880593
5252	ss69127715	G/T	CSHL-HAPMAP	HapMap-YRI	NA18522	YOR016.03	chr13-HapMap-YRI
5259	ss1479967	T/T	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	r23_ch13_YRI_perlegen:genotyping_1.0.0	4880593
5259	ss69127715	G/G	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	chr13-HapMap-YRI
5264	ss1479967	G/G	CSHL-HAPMAP	HapMap-YRI	NA18862	YOR024.03	r23_ch13_YRI_perlegen:genotyping_1.0.0	4880593
5264	ss69127715	G/T	CSHL-HAPMAP	HapMap-YRI	NA18862	YOR024.03	chr13-HapMap-YRI
5280	ss1479967	G/G	CSHL-HAPMAP	HapMap-YRI	NA19173	YOR047.01	r23_ch13_YRI_perlegen:genotyping_1.0.0	4880593
5280	ss69127715	G/T	CSHL-HAPMAP	HapMap-YRI	NA19173	YOR047.01	chr13-HapMap-YRI
5293	ss1479967	T/T	CSHL-HAPMAP	HapMap-YRI	NA19159	YOR056.02	r23_ch13_YRI_perlegen:genotyping_1.0.0	4880593
5293	ss69127715	G/G	CSHL-HAPMAP	HapMap-YRI	NA19159	YOR056.02	chr13-HapMap-YRI
5307	ss1479967	T/T	CSHL-HAPMAP	HapMap-YRI	NA19145	YOR074.01	r23_ch13_YRI_perlegen:genotyping_1.0.0	4880593
5307	ss69127715	G/T	CSHL-HAPMAP	HapMap-YRI	NA19145	YOR074.01	chr13-HapMap-YRI
5309	ss1479967	T/T	CSHL-HAPMAP	HapMap-YRI	NA19144	YOR074.03	r23_ch13_YRI_perlegen:genotyping_1.0.0	4880593
5309	ss69127715	G/T	CSHL-HAPMAP	HapMap-YRI	NA19144	YOR074.03	chr13-HapMap-YRI

Genotype data submitted for	270	samples from	270	individuals	Individual with multiple genotypes submission:	270

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .